Here is what I am seeing....

While in CoverFlow(full screen mode): 
+ Select the Menu button on the Apple's Remote 
++ RB (Remote Buddy) toggles iTunes back to non-fullscreen mode 
++ RB launches the track's options (volume,rating,repeat,shuffle,picture) 
++ The rating option is greyed out (disabled)

Here are two work-arounds to re-enable RB's track ratings menu option. 
1) Skip Right on RB's Music Browser menu option, and then, Skip Left to return to RB's Track menu mode

2) With RB's menu still active, Apple-Tab'ing to another application re-enables RB's track rating option

Here is what would make sense to me: 
+ While in in CoverFlow(full-screen) mode, press Apple Remote's menu button 
++ RB's menu overlays over CoverFlow(full-screen) and remains in the full screen mode 
++ Rate Tracks is automatically enabled 
++ The user rates the track 
++ The user presses Apple Remote's menu button to hide RB's menu

many thanks for a great product

graham